scPDB - 3hdq entry

Protein Data Bank Entry:

PDB ID : 3hdq

Resolution :2.360 Å

Experimental Method : X-ray

Deposition Date : 2009-05-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	Q9RYF1_DEIRA
AC:	Q9RYF1
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	29.270
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.236	705.375

% Hydrophobic	% Polar
35.89	64.11
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	77 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
24.1245	-106.259	73.4552

Binding mode :

What is Poseview ?

2D View
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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C6'	CG	PRO- 84	3.81	0	Hydrophobic	false
C6'	CD1	ILE- 86	3.79	0	Hydrophobic	false
O6'	NE2	HIS- 109	3.18	152.11	H-Bond (Protein Donor)	false
N3	O	PHE- 175	2.94	153.72	H-Bond (Ligand Donor)	false
C1D	CD1	PHE- 176	3.94	0	Hydrophobic	false
C3D	CE2	TYR- 179	3.9	0	Hydrophobic	false
C2D	CD2	TYR- 179	3.68	0	Hydrophobic	false
C2D	CB	THR- 180	4.47	0	Hydrophobic	false
O2D	OG1	THR- 180	3	162.8	H-Bond (Ligand Donor)	false
O3D	NE1	TRP- 184	3.02	144.17	H-Bond (Protein Donor)	false
C4D	CG1	VAL- 195	4.03	0	Hydrophobic	false
C1D	CG2	THR- 196	4.28	0	Hydrophobic	false
C5D	CD	ARG- 198	3.74	0	Hydrophobic	false
O2A	NE	ARG- 198	2.87	153.15	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 198	3.04	140.45	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 198	3.37	0	Ionic (Protein Cationic)	false
C5D	CG2	VAL- 199	4.34	0	Hydrophobic	false
C4'	CE2	TYR- 209	3.87	0	Hydrophobic	false
C4'	CZ	PHE- 210	3.76	0	Hydrophobic	false
O6'	OG1	THR- 294	3.31	154.68	H-Bond (Protein Donor)	false
O4	ND2	ASN- 296	3.07	152.6	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 305	3.3	127.25	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 305	3.43	133.32	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 305	2.85	167.09	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 305	3.8	0	Ionic (Protein Cationic)	false
O1B	OH	TYR- 335	2.83	151.15	H-Bond (Protein Donor)	false
O2B	OH	TYR- 370	2.77	160.1	H-Bond (Protein Donor)	false
O6'	O	HOH- 448	2.79	144.77	H-Bond (Ligand Donor)	false
C1'	C6	FAD- 450	3.77	0	Hydrophobic	false
O4'	O4	FAD- 450	2.8	133.36	H-Bond (Ligand Donor)	false